Re: [AMBER] Aspartate and Glutamate naming in PDB

From: Zalikha Ibrahim <>
Date: Mon, 6 Aug 2012 18:39:29 -0700 (PDT)

Thanks so much f quick reply. 
How about aspartate and glutamate that have high pKa at pH 7? And basically when the ASH and GLH naming being applied?
I should let you know that I previously sent the protein to a web-based software for pKa prediction.


 From: Carlos Simmerling <>
To: AMBER Mailing List <>; Zalikha Ibrahim <>
Sent: Tuesday, August 7, 2012 9:23 AM
Subject: Re: [AMBER] Aspartate and Glutamate naming in PDB
A low pka would mean they are deprotonated at ph 7, so don't change them.
On Aug 6, 2012 9:21 PM, "Zalikha Ibrahim" <> wrote:

> Hi to all Amber user,
> I have a question about the naming of aspartate and glutamate in PDB.
> Please correct me if I wrong.
> Aspartate and Glutamate are recognized in their deprotonated form by
> default in XLeap (ASP and GLU). If I want to simulate the protein in pH 7,
> should I change the name of all aspartate and glutamate residues that has
> low pKa value at pH 7 as ASH and GLH?
> Thanks so much in advance
> Zalikha Ibrahim
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Received on Mon Aug 06 2012 - 19:00:04 PDT
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